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To get a good picture of how the Disk Defragmenter works, imagine all the data on your hard drive were jigsaw puzzle pieces. Suppose you have three puzzles: a lion, a castle, and a ship. Each puzzle starts out nicely packed away in it's own box, so if you want to make the lion puzzle you just grab the lion box. But suppose when you're done making the lion puzzle you just scatter the pieces throughout the three boxes. Then you make the castle puzzle and again scatter the pieces into all three boxes. Before long all three boxes contain a mix of various puzzle pieces. Now if you want to make the lion puzzle you will have to dig through all three boxes to try and find all the pieces you need. Imagine how long that would take!
Unfortunately, this is what happens to the files on your hard drive. A file might start out being a "contiguous" file, which means all the bytes of data that make up that file are collected in one area, much like the puzzles in their own boxes. But in time that file can have it's bytes of data scattered in many pieces all over your hard drive, known as fragmentation. This is largely because Windows tries to use disk space efficiently, so it stores data in the first available empty space it can find. So if it needs to store a 5000 byte file and comes across an empty space 1000 bytes in size, it will fill that space and continue looking for another space to put the remaining 4000 bytes.
The trouble with this is that Windows now has to look all over your hard drive to find the pieces it needs and, like the puzzle example above, this takes time. So the Disk Defragmenter collects all the pieces of data scattered all over your drive and organizes them back into contiguous files, which can give a serious boost to disk access speeds. Plus, starting with Windows 98 the Disk Defragmenter also reorganizes the programs, putting the most frequently used programs on the faster inner sections of the disk, giving an even greater boost to performance.
The CacheMaster Disk Defragmenter optimization options let you change the way Disk Defragmenter reorganizes your programs. The maximum programs setting allows you to set the maximum number of programs that Disk Defragmenter will rearrange. The higher the number, the more programs will be optimized and the better overall disk performance, but at the cost of Disk Defragmenter taking longer to run.
The maximum no-use days option sets the number of days after which a program will no longer be optimized. So if the Disk Defragmenter sees that you haven't used Solitaire in the selected number of days, it will not bother rearraging that program. The idea is that it's useless to rearrange programs that aren't frequently used. Setting a lower number insures that Disk Defragmenter will closely follow your usage patterns, but again at the cost of longer defragmentation times.
Finally, there's the minimum program size setting. This sets the size that a program must be in order to qualify for rearranging. If you set it to 1024 bytes (1 kilobyte) then anything smaller than that will not be rearranged. A smaller number will allow more programs to be rearranged, but again at the cost of a longer defragmentation process.
For another tweak which can impact disk access and help minimize fragmentation see File Allocation Size.